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Pipe or combine output of three awk commands

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# 1  
Old 01-08-2016
Pipe or combine output of three awk commands
What is the correct syntax to pipe or run three awk commands? Basically, using the output of the first awk as input in the second. Then using the output of the second awk in the third. Thank you Smilie.

Code:
awk 'FNR==NR {E[$1]; next }$3 in E {print $3, $5}' panel_genes.txt RefSeqGene.txt > update.txt | awk 'NR==FNR { X[toupper($1)]++ ; next } ; toupper($13) in X' update.txt hg19_annovar_refGene.txt > match.txt | awk -v OFS="\t" '{ sub(/\r/, "") } ; NR==FNR { N=$2 ; sub(/\..*/, "", $2); A[$2]=N; next } ; $2 in A { $2=A[$2] } 1' update.txt match.txt > hg19_refgene.txt

# 2  
Old 01-08-2016
syntax is:

Code:
awk 'awk code here' infile |
  awk 'awk code here ' |
  awk 'awk code here' > outputfile

Don't see why you need it... but go for it.
# 3  
Old 01-09-2016
Try process substitution (you will need to use bash, ksh93 or zsh)
Code:
awk 'script3' <(awk 'script1' infile1a infile1b) <(awk 'script2' infile2a infile2b)

# 4  
Old 01-09-2016
You can't redirect AND pipe a program's output. If you need one step's output saved, try the tee command.
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